James Gray, the shadow Scottish secretary, has resigned after suggesting MSPs should be abolished.
James Gray assumed the role of shadow Scottish secretary last week
The remarks are understood to have infuriated senior Scottish Tories who were pressing for him to go.
Mr Gray, the MP for Wiltshire North, was appointed last week. Epping Forest MP Eleanor Laing will take up the post.
The SNP described the Conservatives as "anti-Scottish to the core". A Tory spokesman had stressed the remarks were not official party policy.
Mr Gray is reported to have suggested getting rid of Members of the Scottish Parliament so that Scottish MPs could deal with Scottish business at Holyrood and UK business at Westminster.
The Nationalists had tabled a motion in the House of Commons calling on the Conservative Party to make clear who spoke on their behalf about Scottish issues.
SNP constitution spokesman Pete Wishart said: "These outrageous comments by the shadow Scottish secretary could normally be dismissed, but this is the man chosen by Michael Howard to represent the Tories on Scottish issues in the House of Commons."
The MP had challenged Mr Howard to reveal whether he backed Mr Gray or Scottish Conservative leader at Holyrood David McLetchie.
In his letter of resignation to Mr Howard, Mr Gray states: "Although I fully support the party's policy on devolution, I understand that the words I used in recent interviews might be open to interpretation.
"I would not want there to be any misunderstanding and I have no wish to embarrass the party in Scotland, or you.
"For this reason I believe the right course for me is to resign."
Mr McLetchie said Mr Gray's position had become "untenable".
"Resignation was the only option since Michael Howard has made it clear that he runs a disciplined and accountable team at Westminster," he said.
Eleanor Laing will take over from Mr Gray
Mr Gray's predecessor, Scottish Conservative Chairman Peter Duncan, added: "The post of shadow secretary of state for Scotland is an extremely important one which we treat with great respect, so the holder of that post must be in a position where they can clearly articulate Conservative policy.
"I have known Eleanor Laing for years and am delighted that she has been appointed. She is born and bred in Scotland and she will be a tireless advocate for our country."
Mrs Laing held the position of shadow Scottish secretary under William Hague's leadership between 2000 and 2001.
She will retain her responsibility for women in addition to the new post.
Liberal Democrat MP Alistair Carmichael said: "The replacement of one south of England MP for another does nothing to hide the terminal decline of the Scottish Conservatives."
Scottish Secretary Alistair Darling said: "James Gray must be the first
shadow secretary of state for Scotland whose term of office did not include setting foot in Scotland, or even Scottish Questions in the House of Commons.
"I look forward to seeing how long the Member for Epping Forrest lasts as shadow secretary of state."
SNP leader Alex Salmond accused the Tories of descending "from comedy to farce".
"They either want to cut Scottish spending, abolish the Scottish Parliament or think Scotland is an 'unattractive' place to live," he said.
"You can't have a credible Scottish spokesperson in such an anti-Scottish party."